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Full information on isolate SA2 (id:1516)

Projects

This isolate is a member of the following projects:

Public isolates
This project contains the isolates that should be publicly available through the public access database.
published_genomes
All isolates with published genome imported in BIGSdb, and validated for scgMLST_S study
Bialek et al 2014_EID
167 isolates from Bialek et al. in which the scgMLST-634 scheme was defined (PMID: 25341126)

Provenance/primary metadata

id
1516
isolate
SA2
aliases
SA2; SB4384
sender
Suzanne Bialek, AP-HP
curator
Auto Tagger
update history
719 updates show details
date entered
2013-03-29
datestamp
2023-01-20
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
QC status
0000
city
Paris
country
France
continent
Europe
source type
Human
host
Human
source details
Blood
infection
Liver abscess
K type
K1
K typing method
PCR

Publication (1)

  • Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg Infect Dis 20:1812-20

Sequence bin

contigs
223
total length
5,719,746 bp
max length
173,207 bp
mean length
25,650 bp
N50
50,483
L50
30
N90
16,391
L90
103
N95
9,414
L95
125
%GC
56.92
Ns
0
gaps
0
loci tagged
4,079

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962899

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Klebsiella pneumoniae Proteobacteria > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Klebsiella > Klebsiella pneumoniae 100%

Analysis performed: 2022-11-02

Kleborate

species
Klebsiella pneumoniae
species_match
strong
virulence_score
5
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Yersiniabactin
ybt 1; ICEKp10
YbST
47
Colibactin
clb 2
CbST
29
Aerobactin
iuc 1
AbST
1
Salmochelin
iro 1
SmST
2
RmpADC
-,rmp 1; KpVP-1
RmST
0,26-1LV
rmpA2
rmpA2_3-47%
wzi
wzi1
K_locus
KL1
K_type
K1
K_locus_problems
none
K_locus_confidence
Very high
K_locus_identity
99.99%
O_locus
O1/O2v2
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
99.13%
Bla_chr
SHV-11.v1^
SHV_mutations
35Q
ybtS
2
ybtX
2
ybtQ
2
ybtP
2
ybtA
2
irp2
6
irp1
6
ybtU
2
ybtT
2
ybtE
2
fyuA
2
clbA
2
clbB
2
clbC
2
clbD
2
clbE
2
clbF
2
clbG
2
clbH
3
clbI
2
clbL
2
clbM
2
clbN
2
clbO
2
clbP
2
clbQ
2
iucA
1
iucB
1
iucC
1
iucD
1
iutA
1
iroB
1
iroC
4
iroD
1
iroN
1
rmpA
54-47%,2
rmpD
-,29
rmpC
-,2

Analysis performed: 2023-07-21; Kleborate v2.3.2

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (143 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (143 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13436 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13415 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental6 (143 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental6 (143 isolates)

Schemes and loci

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